Histone marks enrichment analysis

Question

[gspirito]

Hello everyone, here's my question:

I have a bed file of human genomic coordinates (hg19), and I would like to know whether ChIP-seq peaks for specific histone marks (such as those from ENCODE) are significantly more represented within my test regions compared to a background (another bed file). Is there any tool which would allow me to do that?

Thanks in advance.

[Ankit]

Use bedtools intersect and count the overlapped regions for your two peak files (separately) against hg19 bed file.